New linezolid-like 1,2,4-oxadiazoles active against Gram-positive multiresistant pathogens

A further pocket or conformational plasticity by mapping COX-1 catalytic site through modified-mofezolac structure-inhibitory activity relationships and their antiplatelet behavior

Cyclooxygenase enzymes have distinct roles in cardiovascular, neurological, and neurodegenerative disease. They are differently expressed in different type of cancers. Specific and selective COXs inhibitors are needed to be used alone or in combo-therapies. Fully understand the differences at the catalytic site of the two cyclooxygenase (COX) isoforms is still opened to investigation. Thus, two series of novel compounds were designed and synthesized in fair to good yields using the highly selective COX-1 inhibitor mofezolac as the lead compound to explore a COX-1 zone formed by the polar residues Q192, S353, H90 and Y355, as well as hydrophobic amino acids I523, F518 and L352. According to the structure of the COX-1:mofezolac complex, hydrophobic amino acids appear to have free volume eventually accessible to the more sterically hindering groups than the methoxy linked to the phenyl groups of mofezolac, in particular the methoxyphenyl at C4-mofezolac isoxazole. Mofezolac bears two methoxyphenyl groups linked to C3 and C4 of the isoxazole core ring. Thus, in the novel compounds, one or both methoxy groups were replaced by the higher homologous ethoxy, normal and isopropyl, normal and tertiary butyl, and phenyl and benzyl. Furthermore, a major difference between the two sets of compounds is the presence of either a methyl or acetic moiety at the C5 of the isoxazole. Among the C5-methyl series, 12 (direct precursor of mofezolac) (COX-1 IC50 = 0.076 μM and COX-2 IC50 = 0.35 μM) and 15a (ethoxy replacing the two methoxy groups in 12; COX-1 IC50 = 0.23 μM and COX-2 IC50 > 50 μM) were still active and with a Selectivity Index (SI = COX-2 IC50/COX-1 IC50) = 5 and 217, respectively. The other symmetrically substituted alkoxyphenyl moietis were inactive at 50 μM final concentration. Among the asymmetrically substituted, only the 16a (methoxyphenyl on C3-isoxazole and ethoxyphenyl on C4-isoxazole) and 16b (methoxyphenyl on C3-isoxazole and n-propoxyphenyl on C4-isoxazole) were active with SI = 1087 and 38, respectively. Among the set of compounds with the acetic moiety, structurally more similar to mofezolac (SI = 6329), SI ranged between 1.4 and 943. It is noteworthy that 17b (n-propoxyphenyl on both C3- and C4-isoxazole) were found to be a COX-2 slightly selective inhibitor with SI = 0.072 (COX-1 IC50 > 50 μM and COX-2 IC50 = 3.6 μM). Platelet aggregation induced by arachidonic acid (AA) can be in vitro suppressed by the synthesized compounds, without affecting of the secondary hemostasia, confirming the biological effect provided by the selective inhibition of COX-1. A positive profile of hemocompatibility in relation to erythrocyte and platelet toxicity was observed. Additionally, these compounds exhibited a positive profile of hemocompatibility and reduced cytotoxicity. Quantitative structure activity relationship (QSAR) models and molecular modelling (Ligand and Structure based virtual screening procedures) provide key information on the physicochemical and pharmacokinetic properties of the COX-1 inhibitors as well as new insights into the mechanisms of inhibition that will be used to guide the development of more effective and selective compounds. X-ray analysis was used to confirm the chemical structure of 14 (MSA17).

Fluorinated azoles as effective weapons in fight against methicillin-resistance staphylococcus aureus (MRSA) and its SAR studies

The rapid spread of Methicillin-resistant Staphylococcus aureus (MRSA) and its difficult-to-treat skin and filmsy diseases are making MRSA a threat to human life. The most dangerous feature is the fast emergence of MRSA resistance to all recognized antibiotics, including vancomycin. The creation of novel, effective, and non-toxic drug candidates to combat MRSA isolates is urgently required. Fluorine containing small molecules have taken a centre stage in the field of drug development. Over the last 50 years, there have been a growing number of fluorinated compounds that have been approved since the clinical usage of fluorinated corticosteroids in the 1950 s and fluoroquinolones in the 1980 s. Due to its advantages in terms of potency and ADME (absorption, distribution, metabolism, and excretion), fluoro-pharmaceuticals have been regarded as a potent and useful tool in the rational drug design method. The flexible bioactive fluorinated azoles are ideal candidates for the development of new antibiotics. This review summarizes the decade developments of fluorinated azole derivatives with a wide antibacterial activity against diverged MRSA strains. In specific, we correlated the efficacy of structurally varied fluorinated azole analogues including thiazole, benzimidazole, oxadiazole and pyrazole against MRSA and discussed different angles of structure-activity relationship (SAR).

Identification of N-Acyl Hydrazones as New Non-Zinc-Binding MMP-13 Inhibitors by Structure-Based Virtual Screening Studies and Chemical Optimization

Matrix metalloproteinase 13 plays a central role in osteoarthritis (OA), as its overexpression induces an excessive breakdown of collagen that results in an imbalance between collagen synthesis and degradation in the joint, leading to progressive articular cartilage degradation. Therefore, MMP-13 has been proposed as a key therapeutic target for OA. Here we have developed a virtual screening workflow aimed at identifying selective non-zinc-binding MMP-13 inhibitors by targeting the deep S1' pocket of MMP-13. Three ligands were found to inhibit MMP-13 in the µM range, and one of these showed selectivity over other MMPs. A structure-based analysis guided the chemical optimization of the hit compound, leading to the obtaining of a new N-acyl hydrazone-based derivative with improved inhibitory activity and selectivity for the target enzyme.

Optimization and Antibacterial Evaluation of Novel 3-(5-Fluoropyridine-3-yl)-2-oxazolidinone Derivatives Containing a Pyrimidine Substituted Piperazine

In this study, a series of novel 3-(5-fluoropyridine-3-yl)-2-oxazolidinone derivatives were designed and synthesized based on compounds previously reported, and their antibacterial activity was investigated. Then their antibacterial activity was investigated for the first time. Preliminary screening results showed that all these compounds exhibited antibacterial activity against gram-positive bacteria, including 7 drug-sensitive strains and 4 drug-resistant strains, among which compound 7j exhibited an 8-fold stronger inhibitory effect than linezolid, with a minimum inhibitory concentration (MIC) value of 0.25 µg/mL. Further molecular docking studies predicted the possible binding mode between active compound 7j and the target. Interestingly, these compounds could not only hamper the formation of biofilms, but also have better safety, as confirmed by cytotoxicity experiments. All these results indicate that these 3-(5-fluoropyridine-3-yl)-2-oxazolidinone derivatives have the potential to be developed into novel candidates for the treatment of gram-positive bacterial infections.

Bioisosterism: 1,2,4-Oxadiazole Rings

Although studies in drug discovery have gained momentum in recent years, the conversion of drugs in use today into less toxic derivatives with pharmacologically superior properties is still of great importance in drug research. Bioisosterism facilitates the conversion of drugs into derivatives that present more positive pharmacological and toxicological profiles by changing existing groups in the drug structure within the framework of certain criteria that have been expanded today. The 1,2,4-oxadiazole ring is used as a bioisostere for ester and amide groups due to its resistance to hydrolysis. However, this ring is not limited to esters and amides, but can also be used as a bioisostere for other functional groups. In this review, cases in which the 1,2,4-oxadiazole ring is used as a bioisostere for various functional groups are discussed. Herein we shed light on 1,2,4-oxadiazole bioisosterism in the development of new drug candidates and in enhancing the pharmacological profiles of currently available drugs.

Streptomyces spp. Isolated from Rosa davurica Rhizome for Potential Cosmetic Application

Streptomyces species are widely studied and used in different fields, including antibiotics and pesticides, and are spread in several places as soil-derived microorganisms. However, research on anti-aging, including antioxidants obtained from Streptomyces, has not been performed as much. Skin aging due to bacterial infection, especially methicillin-resistant Staphylococcus aureus (MRSA), is challenging to recover, so it is essential to prevent aging by preventing or inhibiting infection. Therefore, this study was conducted to isolate Streptomyces species from Rosa davurica rhizome soil and to determine the effect of the ethyl acetate extract of the isolated strain Streptomyces chattanoogensis THA-663 (THA-663S) on the inhibition of MRSA and UVB-irradiated human skin keratinocytes, to determine whether it could be a treatment for skin aging. The MRSA inhibition and antioxidant activities were evaluated using disc diffusion, 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2’-azino-bis-(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS), and a reactive oxygen species (ROS) assay. The expression of aging-related markers, including mitogen-activated protein kinases/activator protein 1 (MAPK)/AP-1) and transforming growth factor-β/suppressor of mothers against decapentaplegic (TGF-β/Smad) was assessed using Western blotting. The antibacterial effect on four MRSA strains, CCARM 0204, CCARM 0205, CCARM 3855, and CCARM 3089, showed that THA-663S could greatly inhibit MRSA growth. Moreover, the findings showed that THA-663S is efficient in scavenging free radicals and dose-dependently reducing ROS generation. Furthermore, THA-663S notably reduced UVB-induced matrix metalloproteinase-1 (MMP-1) expression by inhibiting the MAPK/AP-1 signaling pathways and blocking extracellular matrix (ECM) degradation in UVB-irradiated HaCaT cells. Additionally, THA-663S improved and enhanced transforming growth factor-beta (TGF-β) signaling activation to promote procollagen type I synthesis, relieving UVB-induced skin cell damage. In conclusion, THA-663S has a high potential to protect skin cells from aging, and, simultaneously, it can prevent or treat aging caused by infection due to pathogen inhibition.

Synthesis and Biological Evaluation of 3-(Pyridine-3-yl)-2-Oxazolidinone Derivatives as Antibacterial Agents

In this research, a series of 3-(pyridine-3-yl)-2-oxazolidinone derivatives was designed, synthesized, and evaluated for in vitro antibacterial activity, which included bacteriostatic, morphological, kinetic studies, and molecular docking. The results demonstrated that compounds 21b, 21d, 21e and 21f exhibited strong antibacterial activity similar to that of linezolid toward five Gram-positive bacteria. After observing the effect of the drug on the morphology and growth dynamics of the bacteria, the possible modes of action were predicted by molecular docking. Furthermore, the antibiofilm activity and the potential drug resistance assay was proceeded. These compounds exhibited universal antibiofilm activity and compound 21d showed significant concentration-dependent inhibition of biofilm formation. Compound 21d also showed a stable effect on S. pneumoniae (ATCC 49619) with less drug resistance growth for 15 days, which is much longer than that of linezolid. Overall, these results can be used to guide further exploration of novel antimicrobial agents.

A comprehensive review of recent advances in the biological activities of 1,2,4-oxadiazoles

Nitrogen heterocycles play an essential role in medication development. The 1,2,4-oxadiazole heterocycle has been extensively studied, yielding a large variety of molecules with varied biological functions. The 1,2,4-oxadiazole shows bioisosteric equivalency with ester and amide moieties. In recent years, the 1,2,4-oxadiazole nucleus has received a lot of attention in medicinal chemistry. It was thought to be a pharmacophore component in the production of biologically intriguing drugs. This review presents a comprehensive overview of the recent achievements in the biological activities of 1,2,4-oxadiazoles as potential antimicrobial, anticancer, anti-inflammatory, neuroprotective, and antidiabetic agents. The structure-activity relationship and mechanisms of action are also reviewed.

3D-QSAR Studies of 1,2,4-Oxadiazole Derivatives as Sortase A Inhibitors

Sortase A (SrtA) is an enzyme that catalyzes the attachment of proteins to the cell wall of Gram-positive bacterial membrane, preventing the spread of pathogenic bacterial strains. Here, one class of oxadiazole compounds was distinguished as an efficient inhibitor of SrtA via the "S. aureus Sortase A" substrate-based virtual screening. The current study on 3D-QSAR was done by utilizing preparation of the structure in the Schrödinger software suite and an assessment of 120 derivatives with the crystal structure of 1,2,4-oxadiazole which was extracted from the PDB data bank. The docking operation of the best compound in terms of pMIC (pMIC = 2.77) was done to determine the drug likeliness and binding form of 1,2,4-oxadiazole derivatives as antibiotics in the active site. Using the kNN-MFA way, seven models of 3D-QSAR were created and amongst them, and one model was selected as the best. The chosen model based on q 2 (pred_r 2) and R 2 values related to the sixth factor of PLS illustrates better and more acceptable external and internal predictions. Values of crossvalidation (pred_r 2), validation (q 2), and F were observed 0.5479, 0.6319, and 179.0, respectively, for a test group including 24 molecules and the training group including 96 molecules. The external reliability outcomes showed that the acceptable and the selective 3D-QSAR model had a high predictive potential (R 2 = 0.9235) which was confirmed by the Y-randomization test. Besides, the model applicability domain was described successfully to validate the estimation of the model.

Ammonium Formate-Pd/C as a New Reducing System for 1,2,4-Oxadiazoles. Synthesis of Guanidine Derivatives and Reductive Rearrangement to Quinazolin-4-Ones with Potential Anti-Diabetic Activity

1,2,4-Oxadiazole is a heterocycle with wide reactivity and many useful applications. The reactive O-N bond is usually reduced using molecular hydrogen to obtain amidine derivatives. NH4CO2H-Pd/C is here demonstrated as a new system for the O-N reduction, allowing us to obtain differently substituted acylamidine, acylguanidine and diacylguanidine derivatives. The proposed system is also effective for the achievement of a reductive rearrangement of 5-(2'-aminophenyl)-1,2,4-oxadiazoles into 1-alkylquinazolin-4(1H)-ones. The alkaloid glycosine was also obtained with this method. The obtained compounds were preliminarily tested for their biological activity in terms of their cytotoxicity, induced oxidative stress, α-glucosidase and DPP4 inhibition, showing potential application as anti-diabetics.

A key review on oxadiazole analogs as potential methicillin-resistant Staphylococcus aureus (MRSA) activity: Structure-activity relationship studies

Methicillin-resistant Staphylococcus aureus (MRSA) is becoming dangerous to human beings due to easy transmission mode and leading to the difficult-to-treat situation. The rapid resistance development of MRSA to many approved antibiotics is of major concern. There is a lot of scope to develop novel, efficient, specific, and nontoxic drug candidates to fight against MRSA isolates. The interesting molecular structure and adaptable feature of oxadiazole moiety which are bioisosteres of esters and amides, and these functional groups show improved resistance to esterases mediated hydrolytic cleavage, attracting researchers to develop required novel antibiotics based on oxadiazole core. This review summarizes the developments of oxadiazole-containing derivatives as potent antibacterial agents against multidrug-resistant MRSA strains and discussing the structure-activity relationship (SAR) in various directions. The current survey is the highlight of the present scenario of oxadiazole hybrids on MRSA studies, covering articles published from 2011 to 2020. This collective information may become a good platform to plan and develop new oxadiazole-based small molecule growth inhibitors of MRSA with minimal side effects.

Synthesis, antibacterial activities, and sustained perfume release properties of optically active5-hydroxy- and 5-acetoxyalkanethioamide analogues

5-Acetoxy- and 5-hydroxyalkanethioamide analogues showed high antibacterial activity against Staphylococcus aureus. Antibacterial thioamides were prepared from 5-alkyl-δ-lactones by amidation, thionation, and subsequent deacetylation. Optically active thioamides with 99% diastereomeric excesses were prepared by diastereomeric resolution using Cbz-L-proline as the resolving agent. Antibacterial thioamides were slowly lactonized by a lipase catalyst. Therefore, these thioamides are potential sustained-release perfume compounds having antibacterial properties.

Synthesis and biological evaluation of novel indenopyrazole derivatives

A series of novel indenopyrazole derivatives 2a-j and 3a-j were synthesized from the reaction of 1-(4-(hydroxy(1-oxo-1,3-dihydro-2 H-inden-2-ylidene)methyl)phenyl)-3-phenylurea derivatives 1a-j with hydrazine and phenylhydrazine, respectively. The obtained novel indenopyrazoles ( 2a-j and 3a-j) were evaluated for anticancer activity against HeLa and C6 cell lines. Antiproliferative activity was determined by the BrdU proliferation ELISA assay; 2a, 2b, 2d, 2h, and 3h were found to be the most active compounds. The compounds were also screened for antimicrobial activity, and all compounds showed moderate activity against used microorganisms.

Vinyl-1,2,4-oxadiazoles Behave as Nucleophilic Partners in Morita-Baylis-Hillman Reactions

We describe that vinyl-oxadiazoles function as a new and efficient nucleophilic partner for the Morita-Baylis-Hillman (MBH) reaction. The reaction between 5-vinyl-3-aryl-1,2,4-oxadiazoles and aromatic and aliphatic aldehydes, catalyzed by DABCO in the absence of solvent, showed high efficiency to afford a new class of heterocyclic MBH adducts with potential biological activity on yields up to 99% and short reaction times. These synthetically attractive adducts bear a heterocyclic scaffold of large pharmaceutical and commercial interest associated with a plethora of biological effects and technological applications. We also demonstrate their synthetic usefulness by a photoinduced addition reaction to a polyfunctionalized amino alcohol.

Computational and biological profile of boronic acids for the detection of bacterial serine- and metallo-β-lactamases

β-Lactamases (BLs) able to hydrolyze β-lactam antibiotics and more importantly the last resort carbapenems, represent a major mechanism of resistance in Gram-negative bacteria showing multi-drug or extensively drug resistant phenotypes. The early detection of BLs responsible of resistant infections is challenging: approaches aiming at the identification of new BLs inhibitors (BLI) can thus serve as the basis for the development of highly needed diagnostic tools. Starting from benzo-[b]-thiophene-2-boronic acid (BZB), a nanomolar inhibitor of AmpC β-lactamase (K _i  = 27 nM), we have identified and characterized a set of BZB analogues able to inhibit clinically-relevant β-lactamases, including AmpC, Extended-Spectrum BLs (ESBL), KPC- and OXA-type carbapenemases and metallo-β-lactamases (MBL). A multiligand set of boronic acid (BA) β-lactamase inhibitors was obtained using covalent molecular modeling, synthetic chemistry, enzyme kinetics and antibacterial susceptibility testing. Data confirmed the possibility to discriminate between clinically-relevant β-lactamases on the basis of their inhibition profile. Interestingly, this work also allowed the identification of potent KPC-2 and NDM-1 inhibitors able to potentiate the activity of cefotaxime (CTX) and ceftazidime (CAZ) against resistant clinical isolates (MIC reduction, 32-fold). Our results open the way to the potential use of our set of compounds as a diagnostic tool for the sensitive detection of clinically-relevant β-lactamases.

Comparing Drug Images and Repurposing Drugs with BioGPS and FLAPdock: The Thymidylate Synthase Case

Repurposing and repositioning drugs has become a frequently pursued and successful strategy in the current era, as new chemical entities are increasingly difficult to find and get approved. Herein we report an integrated BioGPS/FLAPdock pipeline for rapid and effective off-target identification and drug repurposing. Our method is based on the structural and chemical properties of protein binding sites, that is, the ligand image, encoded in the GRID molecular interaction fields (MIFs). Protein similarity is disclosed through the BioGPS algorithm by measuring the pockets' overlap according to which pockets are clustered. Co-crystallized and known ligands can be cross-docked among similar targets, selected for subsequent in vitro binding experiments, and possibly improved for inhibitory potency. We used human thymidylate synthase (TS) as a test case and searched the entire RCSB Protein Data Bank (PDB) for similar target pockets. We chose casein kinase IIα as a control and tested a series of its inhibitors against the TS template. Ellagic acid and apigenin were identified as TS inhibitors, and various flavonoids were selected and synthesized in a second-round selection. The compounds were demonstrated to be active in the low-micromolar range.

Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic-ribosome complex supervised by experiment and electronic structure methods

We propose several new and promising antibacterial agents for the treatment of serious Gram-positive infections. Our predictions rely on force field simulations, supervised by first principle calculations and available experimental data. Different force fields were tested in order to reproduce linezolid's conformational space in terms of a) the isolated and b) the ribosomal bound state. In a first step, an all-atom model of the bacterial ribosome consisting of nearly 1600 atoms was constructed and evaluated. The conformational space of 30 different ribosomal/oxazolidinone complexes was scanned by stochastic methods, followed by an evaluation of their enthalpic penalties or rewards and the mechanical strengths of the relevant hydrogen bonds (relaxed force constants; compliance constants). The protocol was able to reproduce the experimentally known enantioselectivity favoring the S-enantiomer. In a second step, the experimentally known MIC values of eight linezolid analogues were used in order to crosscheck the robustness of our model. In a final step, this benchmarking led to the prediction of several new and promising lead compounds. Synthesis and biological evaluation of the new compounds are on the way.

Synthesis and biological evaluation of Schiff base-linked imidazolyl naphthalimides as novel potential anti-MRSA agents

Schiff base-linked imidazolyl naphthalimide 9i was a potential anti-MRSA agent, which could effectively inhibit the growth of MRSA.

α-Chymotrypsin superactivity in quaternary ammonium salt solution: kinetic and computational studies

Ammonium salts determine an increase of the hydrophobicity of the α-chymotrypsin catalytic site and therefore an improvement of its activity.

Enhancement of premature stop codon readthrough in the CFTR gene by Ataluren (PTC124) derivatives

Premature stop codons are the result of nonsense mutations occurring within the coding sequence of a gene. These mutations lead to the synthesis of a truncated protein and are responsible for several genetic diseases. A potential pharmacological approach to treat these diseases is to promote the translational readthrough of premature stop codons by small molecules aiming to restore the full-length protein. The compound PTC124 (Ataluren) was reported to promote the readthrough of the premature UGA stop codon, although its activity was questioned. The potential interaction of PTC124 with mutated mRNA was recently suggested by molecular dynamics (MD) studies highlighting the importance of H-bonding and stacking π-π interactions. To improve the readthrough activity we changed the fluorine number and position in the PTC124 fluoroaryl moiety. The readthrough ability of these PTC124 derivatives was tested in human cells harboring reporter plasmids with premature stop codons in H2BGFP and FLuc genes as well as in cystic fibrosis (CF) IB3.1 cells with a nonsense mutation. Maintaining low toxicity, three of these molecules showed higher efficacy than PTC124 in the readthrough of the UGA premature stop codon and in recovering the expression of the CFTR protein in IB3.1 cells from cystic fibrosis patient. Molecular dynamics simulations performed with mutated CFTR mRNA fragments and active or inactive derivatives are in agreement with the suggested interaction of PTC124 with mRNA.

Photo-inhibition of Aβ fibrillation mediated by a newly designed fluorinated oxadiazole

The interaction of oxadiazole3photo-stimulated with Aβ_1–40induces a structural modification responsible for fibrillogenesis inhibition.

Efficient assembly of mono- and bis(1,2,4-oxadiazol-3-yl)furoxan scaffolds via tandem reactions of furoxanylamidoximes

Tandem protocols for the synthesis of new types of hybrid molecules – (1,2,4-oxadiazol-3-yl)furoxans based on the furoxanylamidoximes heterocyclization have been developed.

Hsp60 chaperonopathies and chaperonotherapy: targets and agents

INTRODUCTION

Hsp60 (Cpn60) assembles into a tetradecamer that interacts with the co-chaperonin Hsp10 (Cpn10) to assist client polypeptides to fold, but it also has other roles, including participation in pathogenic mechanisms.

AREA COVERED

Hsp60 chaperonopathies are pathological conditions, inherited or acquired, in which the chaperone plays a determinant etiologic-pathogenic role. These diseases justify selection of Hsp60 as a target for developing agents that interfere with its pathogenic effects. We provide information on how to proceed.

EXPERT OPINION

The information available encourages the development of ways to improve Hsp60 activity (positive chaperonotherapy) when deficient or to block it (negative chaperonotherapy) when pathogenic. Many questions are still unanswered and obstacles are obvious. More information is needed to establish when and why autologous Hsp60 becomes a pathogenic autoantigen, or induces cytokine formation and inflammation, or favors carcinogenesis. Clarification of these points will take considerable time. However, analysis of the Hsp60 molecule and a search for active compounds aimed at structural sites that will affect its functioning should continue without interruption. No doubt that some of these compounds will offer therapeutic hopes and will also be instrumental for dissecting structure-function relationships at the biochemical and biological (using animal models and cultured cells) levels.